Author: bugman
Date: Thu Jun 13 11:18:11 2013
New Revision: 20085
URL: http://svn.gna.org/viewcvs/relax?rev=20085&view=rev
Log:
Added polish to all of the interatom user function docstrings.
Modified:
trunk/user_functions/interatom.py
Modified: trunk/user_functions/interatom.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/interatom.py?rev=20085&r1=20084&r2=20085&view=diff
==============================================================================
--- trunk/user_functions/interatom.py (original)
+++ trunk/user_functions/interatom.py Thu Jun 13 11:18:11 2013
@@ -49,7 +49,7 @@
# The interatom.copy user function.
uf = uf_info.add_uf('interatom.copy')
uf.title = "Copy all data associated with a interatomic data container."
-uf.title_short = "Spin copying."
+uf.title_short = "Interatomic interaction copying."
uf.display = True
uf.add_keyarg(
name = "pipe_from",
@@ -133,7 +133,7 @@
default = True,
py_type = "bool",
desc_short = "directly bonded atoms flag",
- desc = "This is a flag which if True means that the two spins are
directly bonded. This flag is useful to simply the set up of the main
heteronuclear relaxation mechanism or one-bond residual dipolar couplings."
+ desc = "This is a flag which if True means that the two spins are
directly bonded. This flag is useful to simplify the set up of the main
heteronuclear relaxation mechanism or one-bond residual dipolar couplings."
)
uf.add_keyarg(
name = "pipe",
@@ -167,8 +167,8 @@
# The interatom.read_dist user function.
uf = uf_info.add_uf('interatom.read_dist')
-uf.title = "Load the inter-spin distances for the interatomic interactions
from a file."
-uf.title_short = "Interatomic distance loading."
+uf.title = "Read inter-spin distances from a file."
+uf.title_short = "Interatomic distance reading."
uf.add_keyarg(
name = "file",
py_type = "str",
@@ -190,7 +190,7 @@
default = "meter",
py_type = "str",
desc_short = "distance unit",
- desc = "The unit of distance. The default is 'meter', but 'Angstrom'
can also be specified.",
+ desc = "The unit of distance. The default is meter, but Angstrom can
also be specified.",
wiz_element_type = "combo",
wiz_combo_choices = ["meter", "Angstrom"],
wiz_read_only = True
@@ -232,8 +232,8 @@
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This allows interatomic distances to be read from
a file. This is useful in the case when the distances vary, avoiding having
to tediously use the interatom.set_dist user function for each spin-pair
separately. The format of the file should be columnar, with the two spin ID
strings in two separate columns and the distances in any other. The default
measurement unit is 'meter' but this can be changed to 'Angstrom'.")
-uf.desc[-1].add_paragraph("For RDC and relaxation based anylses, as the
magnetic dipole-dipole interaction is averaged in NMR over the interatomic
distance to the inverse third power, the interatomic distances within a 3D
structural file are of no use for defining the interaction. Therefore these
r^-3 average distances must be explicitly defined.")
+uf.desc[-1].add_paragraph("This allows interatomic distances to be read from
a file. This is useful in the case when the distances vary, avoiding having
to tediously use the interatom.set_dist user function for each spin-pair
separately. The format of the file should be columnar, with the two spin ID
strings in two separate columns and the distances in any other. The default
measurement unit is meter but this can be changed to Angstrom.")
+uf.desc[-1].add_paragraph("For RDC and relaxation based analyses, as the
magnetic dipole-dipole interaction is averaged in NMR over the interatomic
distance to the inverse third power, the interatomic distances within a 3D
structural file are of no use for defining the interaction. Therefore these
r^-3 average distances must be explicitly defined.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To load the distances in meters from the fifth
column of the 'distances' file, and where the spin IDs are in the first and
second columns, type one of the following:")
@@ -249,8 +249,8 @@
# The interatom.set_dist user function.
uf = uf_info.add_uf('interatom.set_dist')
-uf.title = "Set the inter-spin distances for the interatomic interactions."
-uf.title_short = "Magnetic dipole-dipole distance setup."
+uf.title = "Set the inter-spin distances."
+uf.title_short = "Interatomic distance setup."
uf.add_keyarg(
name = "spin_id1",
default = "@N",
@@ -286,7 +286,8 @@
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("As the magnetic dipole-dipole interaction is
averaged in NMR over the interatomic distance to the inverse third power, the
interatomic distances within a 3D structural file are of no use for defining
the interaction. Therefore these average distances must be explicitly
supplied. This user function allows these distances to be set up. The
default measurement unit is 'meter' but this can be changed to 'Angstrom'.")
+uf.desc[-1].add_paragraph("For many NMR interactions, the distance between
the spin of interest and another spin or atom must be defined. This
information can be extracted from a 3D structure but, in many cases, these
distances are not of interest. For example the empirical or fixed distance
calculation of proton positions in X-ray crystallographic structures will
often not correspond to the real interatomic distances.")
+uf.desc[-1].add_paragraph("Another example is the magnetic dipole-dipole
interaction which is averaged over the interatomic distance to the inverse
third power. In this case, the interatomic distances from any 3D structural
file can be of no use for defining the interaction. The average distances
must be explicitly supplied. This user function allows these distances to be
set up. The default measurement unit is meter but this can be changed to
Angstrom. Alternatively the distances can be read from a file using other
user functions in this class.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To set the N-H distance for protein the 15N
heteronuclear relaxation mechanism to 1.02 Angstrom, type one of the
following:")
r20085 - /trunk/user_functions/interatom.py